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openmm / pdbfixer

PDBFixer fixes problems in PDB files
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The repair of two ends of peptide didn't return the desired result #283

Open bdx114514 opened 10 months ago

bdx114514 commented 10 months ago

Hi,

I generate a pdb file of a short peptide (without hydrogens) and want to use pdbfixer to repair all the missing atoms. However, the result is not ideal. N-terminal is repaired to -NH3 and C-terminal is repaired to -COO

I have uploaded the script I write and the result. Do I need some additional settings to repair two ends to standard amino and carboxyl？ upload.zip